MolNFT v1 · #78760 · protein + RNA

Structure of a HPRP31-15.5K-U4ATAC 5' stem loop complex, dimeric form

3SIV · NHP2-like protein 1: “Structure of a HPRP31-15.5K-U4ATAC 5' stem loop complex, dimeric form”. X-ray diffraction, 19 pockets (best druggability 0.71). MolNFT v1 #78760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SIV
Type: protein + RNA
Length: 1,584 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NHP2-like protein 1; U4/U6 small nuclear ribonucleoprotein PRP31; U4ATAC snrna
UniProt: P55769, Q8WWY3
Pockets: 19 · best druggability 0.71

Structure

x-ray diffraction · 8 distinct chains · 60% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	NHP2-like protein 1	protein	128	46% helix, 15% strand	P55769
B	U4/U6 small nuclear ribonucleoprotein PRP31	protein	237	70% helix, 0% strand	Q8WWY3
C, F, I, L	U4ATAC snrna	rna	32	—	—
D	NHP2-like protein 1	protein	125	45% helix, 14% strand	P55769
E	U4/U6 small nuclear ribonucleoprotein PRP31	protein	236	72% helix, 0% strand	Q8WWY3
H	U4/U6 small nuclear ribonucleoprotein PRP31	protein	235	57% helix, 0% strand	Q8WWY3
J	NHP2-like protein 1	protein	126	47% helix, 16% strand	P55769
K	U4/U6 small nuclear ribonucleoprotein PRP31	protein	241	63% helix, 0% strand	Q8WWY3

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.71	0.90	29	empty
2	62	0.58	0.89	17	empty
3	161	0.54	0.81	18	empty
4	287	0.52	0.75	29	empty
5	126	0.51	0.81	18	empty

Interfaces

26 interfaces between chains.

I–L · 1838 Å² buried · 161 hydrogen bonds · nucleic-nucleic
C–F · 1830 Å² buried · 156 hydrogen bonds · nucleic-nucleic
B–F · 603 Å² buried · 16 hydrogen bonds · protein-nucleic
H–L · 593 Å² buried · 13 hydrogen bonds · protein-nucleic
A–B · 574 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3SIV · Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P55769
Every structure of UniProt Q8WWY3
Elsewhere: RCSB PDB 3SIV · PDBe 3SIV · UniProt P55769 · UniProt Q8WWY3

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